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Next generation nanoLC-MS/MS-based proteomics on high-resolution, high-speed mass spectrometry platforms allows for unbiased profiling of protein (variant) expression, and may substantially expand our ability to understand the association between cancer-related genomic variation and cancer phenotypes.



The current infrastructure consists of 3 nano-liquid chromatografy systems on-line coupled to tandem mass spectrometers (see figure proteomics infrastructure):

  • 3 Orbitrap platforms (2x QExactive and 1x QExactive HF, all ThermoFisher)

Tandem mass spectrometers at the OPL (CCA 1-47). Left: next generation Orbitrap, the QExactive (ThermoFisher) (one of the systems is shown). Right: nanoLC system (Ultimate3000) coupled to a QTrap 5500 platform (Applied Biosystems).



IT Infrastructure

After data acquisition by nanoLC-MS/MS, raw data are processed by the software tool MaxQuant for peptide/protein identification and quantification. For large-scale projects, we employ the IDPicker tool to integrate database search results from multiple search engines, including MS-GF+ and Myrimatch, for identification and quantification. Data exports to Excel are used for further dedicated statistical analyses, which is also facilitated by the OPL.

The computer infrastructure to cope with the large data flows is constantly being upgraded. Currently, three servers are in a local network with the tandem MS data acquisition PCs and are connected to the VUmc network via a network switch.  These servers are connected to the VUmc store4ever system for big data storage, as well as VUmc GreenQloud and the national life science grid for additional computing power.


| Infrastructure | Forms & Protocols | Software | Education | Tutorial figures | OPL meetings |








| Infrastructure | Forms & Protocols | Software | Education | Tutorial figuresOPL meetings |





 | Infrastructure | Forms & Protocols | Software | Education | Tutorial figures | OPL meetings |



The OPL organizes every year an optional VUmc master course entitled: 'Biomedical Proteomics' of 2 weeks that runs end of January-early February. It encompasses both lectures and practical work. It is intended for VUmc master students and our collaborators who wish to obtain more in-depth knowledge of proteomics. See here for the schedule of 2015.

More information for master students.



see also from VU University website


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Protein identification by mass spectrometry-based proteomics


Biomarker discovery and validation pipeline

Process flow for the development of novel biomarker candidates. Each of the five biomarker development phases has its specific aims and requirements. Experiment size refers to the numbers of proteins expected to be evaluated as candidate biomarkers in each phase of development in relation to the sample requirements. Adapted from Suriniva et al., J.Proteome.Res. 10(1), 5-16 (7-1-2011).




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OPL meetings